SAXSdb — 1w0s

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROPERDIN

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 28–469	Fragment：RESIDUES 28-469	No other associated polymer	SOLUTION SCATTERING mmCIF provides none of the parsed experimental conditions	Resolution not provided
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 28–469	Fragment：RESIDUES 28-469	No other associated polymer	SOLUTION SCATTERING mmCIF provides none of the parsed experimental conditions	Resolution not provided
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 28–469	Fragment：RESIDUES 28-469	No other associated polymer	SOLUTION SCATTERING mmCIF provides none of the parsed experimental conditions	Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1W0S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1W0R Solution structure of dimeric form of properdin by X-ray solution scattering and analytical ultracentrifugation Deposited 2004-06-09	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–469（442 aa） Fragment：RESIDUES 28-469	Not recorded	No recorded non-water small molecule	SOLUTION SCATTERING mmCIF provides none of the parsed conditions	Resolution not provided
1W0R Solution structure of dimeric form of properdin by X-ray solution scattering and analytical ultracentrifugation Deposited 2004-06-09	Parsed fields agree	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–469（442 aa） Fragment：RESIDUES 28-469	Not recorded	No recorded non-water small molecule	SOLUTION SCATTERING mmCIF provides none of the parsed conditions	Resolution not provided
6RUR Structure of the SCIN stabilized C3bBb convertase bound to properdin Deposited 2019-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain U 28–255（228 aa） Chain V 256–469（214 aa） Chain X 28–255（228 aa） Chain Y 256–469（214 aa）	Mutation：TSR2 and TSR3 are not modelled Mutation：TSR2 and TSR3 are not modelled	MAN alpha-D-mannopyranose × 18 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；50 mM MgAcetate 50 mM Mes 6.5 5 % w/v PEG 10K	Resolution 6.00 Å R-free 0.272
6RUS Structure of a functional properdin monomer Deposited 2019-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–255（228 aa）	Not recorded	MAN alpha-D-mannopyranose × 8 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；1.1 M ammonium sulfate, 0.1 M sodium acetate pH 6.0, 1.2%(w/v) myo-inositol	Resolution 2.80 Å R-free 0.274
6RUS Structure of a functional properdin monomer Deposited 2019-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 256–469（214 aa）	Not recorded	MAN alpha-D-mannopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；1.1 M ammonium sulfate, 0.1 M sodium acetate pH 6.0, 1.2%(w/v) myo-inositol	Resolution 2.80 Å R-free 0.274
6RUV Structure of the SCIN stabilized C3bBb convertase bound to Properdin and a the non-inhibitory nanobody hFPNb1 Deposited 2019-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain U 28–191（164 aa） Chain V 256–469（214 aa） Chain X 28–191（164 aa） Chain Y 256–469（214 aa）	Not recorded	MAN alpha-D-mannopyranose × 21 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；277 K；100 mM NaCl, 5 % (w/v) PEG4000, 10 mM MgCl2, 100 mM Sodium Cacodylate trihydrate pH 5.8.	Resolution 6.15 Å R-free 0.271
6RV6 Structure of properdin lacking TSR3 based on anomalous data Deposited 2019-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–191（164 aa） Chain B 256–469（214 aa）	Not recorded	MAN alpha-D-mannopyranose × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；292 K；1.0 M lithium sulfate, 0.1 M sodium acetate pH 4.0, 0.1 M barium chloride	Resolution 3.51 Å R-free 0.283
6S08 Crystal Structure of Properdin (TSR domains N1 & 456) Deposited 2019-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 256–469（214 aa） Chain B 26–132（107 aa）	Not recorded	MAN alpha-D-mannopyranose × 8 PGE TRIETHYLENE GLYCOL × 1 NA SODIUM ION × 1 FUC alpha-L-fucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Potassium Sulphate, PEG 3350	Resolution 2.03 Å R-free 0.248
6S0A Crystal Structure of Properdin (TSR domains N12 & 456) Deposited 2019-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 256–469（214 aa） Chain B 26–191（166 aa）	Not recorded	MAN alpha-D-mannopyranose × 10 FUC alpha-L-fucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；Sodium Citrate, PEG 3000	Resolution 2.52 Å R-free 0.267
6S0B Crystal Structure of Properdin in complex with the CTC domain of C3/C3b Deposited 2019-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 256–469（214 aa） Chain B 26–132（107 aa）	Not recorded	MAN alpha-D-mannopyranose × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；Tacsimate, PEG 3350	Resolution 2.31 Å R-free 0.277
6SEJ Structure of a functional monomeric properdin lacking TSR3 Deposited 2019-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–191（164 aa） Chain B 256–469（214 aa）	Not recorded	MAN alpha-D-mannopyranose × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；292 K；1.0 M lithium sulfate, 0.1 M sodium acetate pH 4.0, 0.1 M barium chloride	Resolution 3.50 Å R-free 0.266
7B26 CirpA1 in complex with pseudo-monomeric Properdin lacking TSR2-3 Deposited 2020-11-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–134（134 aa） Chain B 256–469（214 aa）	Not recorded	MAN alpha-D-mannopyranose × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M Potassium thiocyanate, 0.1 M Tris, pH 7.5, 18 % w/v PEG 5000 MME	Resolution 3.40 Å R-free 0.274
7NOZ Structure of the nanobody stablized properdin bound alternative pathway proconvertase C3b:FB:FP Deposited 2021-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 28–190（163 aa） Chain D 255–461（207 aa）	Not recorded	MAN alpha-D-mannopyranose × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Na-acetate pH 5.3, 0.1 M Mg-formate,7% PEG5000 MME	Resolution 3.90 Å R-free 0.265
8Q6R Structure of complement FP in complex with the TPP-3077 VHH Deposited 2023-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 28–135（108 aa） Chain D 256–469（214 aa）	Not recorded	GCH GLYCOCHOLIC ACID × 2 MAN alpha-D-mannopyranose × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；95% Morpheus Screen III, condition G1	Resolution 1.90 Å R-free 0.238
8Q6R Structure of complement FP in complex with the TPP-3077 VHH Deposited 2023-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 28–135（108 aa） Chain F 256–469（214 aa）	Not recorded	MAN alpha-D-mannopyranose × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；95% Morpheus Screen III, condition G1	Resolution 1.90 Å R-free 0.238
9U62 AP pathways C3 convertase C3bBbP and C3 complex Deposited 2025-03-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain P 1–453（453 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 NI NICKEL (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

13 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PROP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–442； UniProt 28–469 Author chain B； PDBConstruct 1–442； UniProt 28–469 Author chain C； PDBConstruct 1–442； UniProt 28–469

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1w0s
Deposition date deposition_date	2004-06-09
Structure title title	Solution structure of trimeric form of properdin by X-ray solution scattering and analytical ultracentrifugation
Keywords keywords	X-RAY SCATTERING, ANALYTICAL ULTRACENTRIFUGATION, COMPLEMENT, THROMBOSPONDIN TYPE I REPEATS, CONSTRAINED MODELLING, GLYCOPROTEIN; GLYCOPROTEIN
Experimental Method method	SOLUTION SCATTERING

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	— Å
Radius of gyration Rg (electron density) rg_electron	103.00 Å
Forward intensity I(0) i0	357218000.00
Molecular weight molecular_weight	145480.0 kDa
Excluded volume excluded_volume	173660 Å³
Envelope volume envelope_volume	444560 Å³
Hydration-shell volume shell_volume	41760 Å³
Envelope diameter envelope_diameter	289.7 Å
Shell Rg shell_rg	70.91 Å
Envelope Rg envelope_rg	93.29 Å
Shape Rg shape_rg	102.50 Å
Total Rg total_rg	102.60 Å
Total atoms total_atoms	—
Residues n_residues	—
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	251.0 Å
Rg (real space) rg_real	97.78 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	3.4160e+08
I(0) uncertainty (real space) i0_real_error	6.9100e+06
Rg (reciprocal space) rg_reciprocal	98.31 Å
I(0) (reciprocal space) i0_reciprocal	353100000.0000
Solution quality estimate total_estimate	0.8877
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	150.6 Å
Skewness Skewness skewness	-0.003
Kurtosis Kurtosis kurtosis	-1.070
Angular range angular_range	— – 0.0750 Å⁻¹
Current regularization parameter α current_alpha	0.9758
Highest regularization parameter α highest_alpha	69140000.0000
Real-space data points n_real_points	16
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.993; Stabil: 0.921; Sysdev: 1.000; Positv: 1.000; Valcen: 0.803; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	3

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	PROPERDIN
Molecular weight formula_weight	48554.0 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	1326

fit	/app/data/saxs_computation/w0/1w0s/1w0s.fit
pddf	/app/data/pr_computation/w0/1w0s/1w0s.pr.out
profile	/app/data/saxs_computation/w0/1w0s/1w0s.dat

Solution structure of trimeric form of properdin by X-ray solution scattering and analytical ultracentrifugation

1. Protein Identity and Related Structures Protein Identity & Related Structures

PROPERDIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)